Neutral and Charged 1-Butyl-3-methylimidazolium Triflate Clusters: Equilibrium Concentration in the Vapor Phase and Thermal Properties of Nanometric Droplets

Ground state energy, structure, and harmonic vibrational modes of 1-butyl-3-methylimidazolium triflate ([bmim][Tf]) clusters have been computed using an all-atom empirical potential model. Neutral and charged species have been considered up to a size (30 [bmim][Tf] pairs) well into the nanometric range. Free energy computations and thermodynamic modeling have been used to predict the equilibrium composition of the vapor phase as a function of temperature and density. The results point to a nonnegligible concentration of very small charged species at pressures (P ~ 0.01 Pa) and temperatures (T 600 K) at the boundary of the stability range of [bmim][Tf]. Thermal properties of nanometric neutral droplets have been investigated in the 0 T 700 K range. A near-continuous transition between a liquidlike phase at high T and a solidlike phase at low T takes place at T ~ 190 K in close correspondence with the bulk glass point Tg ~ 200 K. Solidification is accompanied by a transition in the dielectric properties of the droplet, giving rise to a small permanent dipole embedded into the solid cluster. The simulation results highlight the molecular precursors of several macroscopic properties and phenomena and point to the close competition of Coulomb and dispersion forces as their common origin.

Thermodynamic Studies of Ionic Interactions in Aqueous Solutions of Imidazolium-Based Ionic Liquids [Emim][Br] and [Bmim][Cl]

Experimental measurements of density at different temperatures ranging from 293.15 to 313.15 K, the speed of sound and osmotic coefficients at 298.15 K for aqueous solution of 1-ethyl-3-methylimidazolium bromide ([Emim][Br]), and osmotic coefficients at 298.15 K for aqueous solutions of 1-butyl-3-methylimidazolium chloride ([Bmim][Cl]) in the dilute concentration region are taken. The data are used to obtain compressibilities, expansivity, apparent and limiting molar properties, internal pressure, activity, and activity coefficients for [Emim][Br] in aqueous solutions. Experimental activity coefficient data are compared with that obtained from Debye-Hückel and Pitzer models. The activity data are further used to obtain the hydration number and the osmotic second virial coefficients of ionic liquids. Partial molar entropies of [Bmim][Cl] are also obtained using the free-energy and enthalpy data. The distance of the closest approach of ions is estimated using the activity data for ILs in aqueous solutions and is compared with that of X-ray data analysis in the solid phase. The measured data show that the concentration dependence for aqueous solutions of [Emim][Br] can be accounted for in terms of the hydrophobic hydration of ions and that this IL exhibits Coulombic interactions as well as hydrophobic hydration for both the cations and anions. The small hydration numbers for the studied ILs indicate that the low charge density of cations and their hydrophobic nature is responsible for the formation of the water-structure-enforced ion pairs.

Effect of solution pH, ionic strength, and temperature on adsorption behavior of reactive dyes on activated carbon

The adsorption behavior of C.I. Reactive Blue 2, C.I. Reactive Red 4, and C.I. Reactive Yellow 2 from aqueous solution onto activated carbon was investigated under various experimental conditions. The adsorption capacity of activated carbon for reactive dyes was found to be relatively high. At pH 7.0 and 298 K, the maximum adsorption capacity for C.I. Reactive Blue 2, C.I. Reactive Yellow 2 and C.I. Reactive Red 4 dyes was found to be 0.27, 0.24, and 0.11 mmol/g, respectively. The shape of the adsorption isotherms indicated an L2-type isotherm according to the Giles and Smith classification. The experimental adsorption data showed good correlation with the Langmuir and Ferundlich isotherm models. Further analysis indicated that the formation of a complete monolayer was not achieved, with the fraction of surface coverage found to be 0.45, 0.42, and 0.22 for C.I. Reactive Blue 2, C.I. Reactive Yellow 2 and C.I. Reactive Red 4 dyes, respectively. Experimental data indicated that the adsorption capacity of activated carbon for the dyes was higher in acidic rather than in basic solutions, and further indicated that the removal of dye increased with increase in the ionic strength of solution, this was attributed to aggregation of reactive dyes in solution. Thermodynamic studies indicated that the adsorption of reactive dyes onto activated carbon was an endothermic process. The adsorption enthalpy (?H) for C.I. Reactive Blue 2 and C.I. Reactive Yellow 2 dyes were calculated at 42.2 and 36.2 kJ/mol, respectively. The negative values of free energy (?G) determined for these systems indicated that adsorption of reactive dyes was spontaneous at the temperatures under investigation (298-328 K). © 2007 Elsevier Ltd. All rights reserved.

Scaling of Superdomain Bands in Ferroelectric Dots

Bundles of 90° stripe domains have been observed to form into distinct groups, or bands, in mesoscale BaTiO3 single crystal dots. Vector piezoresponse force microscopy (PFM) shows that each band region, when considered as a single entity, possesses a resolved polarization that lies approximately along the pseudocubic direction; antiparallel alignment of this resultant polarization in adjacent bands means that these regions can be considered as 180° “superdomains.” For dots with sidewall dimensions below ~2 microns, Landau–Kittel like scaling in the width of these superdomains was observed, strongly suggesting that they form in response to lateral depolarizing fields. In larger dot structures, scaling laws break down. We have rationalized these observations by considering changes in the driving force for the adoption of equilibrium superdomain periodicities implied by Landau–Kittel-free energy models; we conclude that the formation of ordered bands of superdomains is a uniquely meso/nanoscale phenomenon. We also note that the superdomain bands found by PFM imaging in air contrast with the quadrant arrangements seen previously by Schilling et al. (Nano Lett., 9, 3359 (2009)) through transmission electron microscopy imaging in vacuum. The importance of the exact nature of the boundary conditions in determining the domain patterns that spontaneously form in nanostructures is therefore clearly implied.

Molecular dynamics and principal components analysis of human telomeric quadruplex multimers.

Guanine-rich DNA repeat sequences located at the terminal ends of chromosomal DNA can fold in a sequence-dependent manner into G-quadruplex structures, notably the terminal 150–200 nucleotides at the 3' end, which occur as a single-stranded DNA overhang. The crystal structures of quadruplexes with two and four human telomeric repeats show an all-parallel-stranded topology that is readily capable of forming extended stacks of such quadruplex structures, with external TTA loops positioned to potentially interact with other macromolecules. This study reports on possible arrangements for these quadruplex dimers and tetramers, which can be formed from 8 or 16 telomeric DNA repeats, and on a methodology for modeling their interactions with small molecules. A series of computational methods including molecular dynamics, free energy calculations, and principal components analysis have been used to characterize the properties of these higher-order G-quadruplex dimers and tetramers with parallel-stranded topology. The results confirm the stability of the central G-tetrads, the individual quadruplexes, and the resulting multimers. Principal components analysis has been carried out to highlight the dominant motions in these G-quadruplex dimer and multimer structures. The TTA loop is the most flexible part of the model and the overall multimer quadruplex becoming more stable with the addition of further G-tetrads. The addition of a ligand to the model confirms the hypothesis that flat planar chromophores stabilize G-quadruplex structures by making them less flexible.

Volumetric properties and enthalpies of solution of alcohols CkH2k+1OH (k = 1, 2, 6) in 1-methyl-3-alkylimidazolium bis(trifluoromethylsulfonyl)imide {[C1CnIm][NTf2] n = 2, 4, 6, 8, 10} ionic liquids

We present a study on the effect of the alkyl chain length of the imidazolium ring in 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids, [C1CnIm][NTf2] (n = 2 to 10), on the mixing properties of (ionic liquid + alcohol) mixtures (enthalpy and volume). We have measured small excess molar volumes with highly asymmetric curves as a function of mole fraction composition (S-shape) with more negative values in the alcohol-rich regions. The excess molar volumes increase with the increase of the alkyl-chain length of the imidazolium cation of the ionic liquid. The values of the partial molar excess enthalpy and the enthalpy of mixing are positive and, for the case of methanol, do not vary monotonously with the length of the alkyl side-chain of the cation on the ionic liquid – increasing from n = 2 to 6 and then decreasing from n = 8. This non-monotonous variation is explained by a more favourable interaction of methanol with the cation head group of the ionic liquid for alkyl chains longer than eight carbon atoms. It is also observed that the mixing is less favourable for the smaller alcohols, the enthalpy of mixing decreasing to less positive values as the alkyl chain of the alcohol increases. Based on the data from this work and on the knowledge of the vapour pressure of {[C1CnIm][NTf2] + alcohol} binary mixtures at T = 298 K reported in the literature, the excess Gibbs free energy, excess enthalpy and excess entropy could be then calculated and it was observed that these mixtures behave like the ones constituted by a non-associating and a non-polar component, with its solution behaviour being determined by the enthalpy.

Understanding the Performance of Melt-Extruded Poly(ethylene oxide)–Bicalutamide Solid Dispersions: Characterisation of Microstructural Properties Using Thermal, Spectroscopic and Drug Release Methods

In this article, we have prepared hot-melt-extruded solid dispersions of bicalutamide (BL) using poly(ethylene oxide) (PEO) as a matrix platform. Prior to preparation, miscibility of PEO and BL was assessed using differential scanning calorimetry (DSC). The onset of BL melting was signi?cantly depressed in the presence of PEO, and using Flory– Huggins (FH) theory, we identi?ed a negative value of -3.4, con?rming miscibility. Additionally, using FH lattice theory, we estimated the Gibbs free energy of mixing which was shown to be negative, passing through a minimum at a polymer fraction of 0.55. Using these data, solid dispersions at drug-to-polymer ratios of 1:10, 2:10 and 3:10 were prepared via hot-melt extrusion. Using a combination of DSC, powder X-ray diffractometry and scanning electron
microscopy, amorphous dispersions of BL were con?rmed at the lower two drug loadings. At the 3:10 BL to PEO ratio, crystalline BL was detected. The percent crystallinity of PEO was reduced by approximately 10% in all formulations following extrusion. The increased amorphous content within PEO following extrusion accommodated amorphous BL at drug to polymer loadings up to 2:10; however, the increased amorphous domains with PEO following extrusion were not suf?cient to fully accommodate BL at drug-to-polymer ratios of 3:10.

Reaction Mechanisms of Crotonaldehyde Hydrogenation on Pt(111): Density Functional Theory and Microkinetic Modeling

The microkinetics based on density function theory (DFT) calculations is utilized to investigate the reaction mechanism of crotonaldehyde hydrogenation on Pt(111) in the free energy landscape. The dominant reaction channel of each hydrogenation product is identified. Each of them begins with the first surface hydrogenation of the carbonyl oxygen of crotonaldehyde on the surface. A new mechanism, 1,4-addition mechanism generating enols (butenol), which readily tautomerize to saturated aldehydes (butanal), is identified as a primary mechanism to yield saturated aldehydes instead of the 3,4-addition via direct hydrogenation of the ethylenic bond. The calculation results also show that the full hydrogenation product, butylalcohol, mainly stems from the deep hydrogenation of surface open-shell dihydrogenation intermediates. It is found that the apparent barriers of the dominant pathways to yield three final products are similar on P(111), which makes it difficult to achieve a high selectivity to the desired crotyl alcohol (COL).

Domain annihilation due to temperature and thickness gradients in single-crystal BaTiO3

The manner in which 90? ferroelectric-ferroelastic domains respond to changes in temperature has been mapped in BaTiO3 single crystals using atomic force microscopy. Domain periodicity remains unaltered until approximately 2 ? C below the Curie temperature (TC ), whereupon domains coarsened dramatically. This behavior was successfully rationalized by considering the temperature dependence of the parameters associated with standard models of ferroelastic domain formation. However, while successful in describing the expected radical increase in equilibrium period with temperature, the model did not predict the unusual mechanism by which domain coarsening occurred; this was not continuous at a local level but instead involved discrete domain annihilation events. Subsequent insights from a combination of free energy analysis for the system and further experimental data from an analogous situation, in which domain period increases with increasing crystal thickness, suggested that domain annihilation is inevitable whenever a component of the relevant gradient that affects domain period is orientated parallel to the domain walls. Consistent with this thesis, we note that, for the observations presented herein, the thermal gradient possessed a significant component parallel to the domain walls. We suggest that domain annihilation is a general feature of domain structures in gradient fields.

Interfacial Properties of LiTFSI and LiPF6-Based Electrolytes in Binary and Ternary Mixtures of Alkylcarbonates on Graphite Electrodes and Celgard Separator

For a better understanding of the adsorption behavior of alkylcarbonate-based electrolytes on graphite electrodes and Celgard separator for Li-ion batteries applications, the interface parameters are determined by contact angle and surface tension measurements. The correlation between these parameters and chemical compositions made of alkyl carbonate with a varying nature of lithium salts (LiPF6 and LiTFSI) and volume fractions of binary and ternary mixtures containing propylene carbonate (PC), ethylene carbonate (EC), and dimethyl carbonate (DMC) is investigated. From the obtained contact angle and surface tension (?L) values for each liquid, the dispersive and polar components of the surface tension (?Ld and ?Lp) of the electrolyte and interfacial free energy between the solid and liquid (?SL) were then calculated using the Young’s equation. The variation of contact angle (?) and the surface tension, as well as the work of adhesion (WA) of binary PC/DMC mixtures on PP, PE, and PET model surfaces were also measured and commented as function of volume fraction of PC in DMC. Finally, the Zisman’s critical surface tension (?C) for studied surfaces was then obtained showing positives slopes of cos ? versus ?L. This behavior is explained by a relative higher adsorption of alkylcarbonates to the hydrogenated supports or graphite. These results are decisive to understand the performance of electrolyte/electrode material/separator interfaces in lithium-ion battery devices.

Comparison of Dynamics of Extracellular Accesses to the β(1) and β(2) Adrenoceptors Binding Sites Uncovers the Potential of Kinetic Basis of Antagonist Selectivity.

From the molecular mechanism of antagonist unbinding in the ß(1) and ß(2) adrenoceptors investigated by steered molecular dynamics, we attempt to provide further possibilities of ligand subtype and subspecies selectivity. We have simulated unbinding of ß(1) -selective Esmolol and ß(2) -selective ICI-118551 from both receptors to the extracellular environment and found distinct molecular features of unbinding. By calculating work profiles, we show different preference in antagonist unbinding pathways between the receptors, in particular, perpendicular to the membrane pathway is favourable in the ß(1) adrenoceptor, whereas the lateral pathway involving helices 5, 6 and 7 is preferable in the ß(2) adrenoceptor. The estimated free energy change of unbinding based on the preferable pathway correlates with the experimental ligand selectivity. We then show that the non-conserved K347 (6.58) appears to facilitate in guiding Esmolol to the extracellular surface via hydrogen bonds in the ß(1) adrenoceptor. In contrast, hydrophobic and aromatic interactions dominate in driving ICI-118551 through the easiest pathway in the ß(2) adrenoceptor. We show how our study can stimulate design of selective antagonists and discuss other possible molecular reasons of ligand selectivity, involving sequential binding of agonists and glycosylation of the receptor extracellular surface. © 2012 John Wiley & Sons A/S.

Excess electron interactions with solvated DNA nucleotides:Strand breaks possible at room temperature

When biological matter is subjected to ionizing radiation, a wealth of secondary low-energy (<20 eV) electrons are produced. These electrons propagate inelastically, losing energy to the medium until they reach energies low enough to localize in regions of high electron affinity. We have recently shown that in fully solvated DNA fragments, nucleobases are particularly attractive for such excess electrons. The next question is what is their longer-term effect on DNA. It has been advocated that they can lead to strand breaks by cleavage of the phosphodiester C-3'-O-3' bond. Here we present a first-principles study of free energy barriers for the cleavage of this bond in fully solvated nucleotides. We have found that except for dAMP, the barriers are on the order of 6 kcal/mol, suggesting that bond cleavage is a regular feature at 300 K. Such low barriers are possible only as a result of solvent and thermal fluctuations. These findings support the notion that low-energy electrons can indeed lead to strand breaks in DNA.

Construction of Drug–Polymer Thermodynamic Phase Diagrams Using Flory–Huggins Interaction Theory: Identifying the Relevance of Temperature and Drug Weight Fraction to Phase Separation within Solid Dispersions

Amorphous drug-polymer solid dispersions have the potential to enhance the dissolution performance and thus bioavailability of BCS class II drug compounds. The principle drawback of this approach is the limited physical stability of amorphous drug within the dispersion. Accurate determination of the solubility and miscibility of drug in the polymer matrix is the key to the successful design and development of such systems. In this paper, we propose a novel method, based on Flory-Huggins theory, to predict and compare the solubility and miscibility of drug in polymeric systems. The systems chosen for this study are (1) hydroxypropyl methylcellulose acetate succinate HF grade (HPMCAS-HF)-felodipine (FD) and (2) Soluplus (a graft copolymer of polyvinyl caprolactam-polyvinyl acetate-polyethylene glycol)-FD. Samples containing different drug compositions were mixed, ball milled, and then analyzed by differential scanning calorimetry (DSC). The value of the drug-polymer interaction parameter ? was calculated from the crystalline drug melting depression data and extrapolated to lower temperatures. The interaction parameter ? was also calculated at 25 °C for both systems using the van Krevelen solubility parameter method. The rank order of interaction parameters of the two systems obtained at this temperature was comparable. Diagrams of drug-polymer temperature-composition and free energy of mixing (?G mix) were constructed for both systems. The maximum crystalline drug solubility and amorphous drug miscibility may be predicted based on the phase diagrams. Hyper-DSC was used to assess the validity of constructed phase diagrams by annealing solid dispersions at specific drug loadings. Three different samples for each polymer were selected to represent different regions within the phase diagram

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.

Locating binding poses in protein-ligand systems using reconnaissance metadynamics

A molecular dynamics-based protocol is proposed for finding and scoring protein-ligand binding poses. This protocol uses the recently developed reconnaissance metadynamics method, which employs a self-learning algorithm to construct a bias that pushes the system away from the kinetic traps where it would otherwise remain. The exploration of phase space with this algorithm is shown to be roughly six to eight times faster than unbiased molecular dynamics and is only limited by the time taken to diffuse about the surface of the protein. We apply this method to the well-studied trypsin-benzamidine system and show that we are able to refind all the poses obtained from a reference EADock blind docking calculation. These poses can be scored based on the length of time the system remains trapped in the pose. Alternatively, one can perform dimensionality reduction on the output trajectory and obtain a map of phase space that can be used in more expensive free-energy calculations.